(CNSNews.com) – President Obama issued a statement Wednesday rejecting several provisions of the 2013 National Defense Authorization Act (NDAA), including a conscience protection for military chaplains that he called “ill-advised”.

“Section 533 is an unnecessary and ill-advised provision, as the military already appropriately protects the freedom of conscience of chaplains and service members,” he said in his signing statement.

Obama made clear that his administration would remain unmoved by the NDAA’s conscience provision, stating that the Department of Defense would continue to implement the repeal of the military’s ban on homosexual service members.

“My Administration remains fully committed to continuing the successful implementation of the repeal of Don't Ask, Don't Tell, and to protecting the rights of gay and lesbian service members; Section 533 will not alter that.”

The president said that the Secretary of Defense would ensure that no “discriminatory” actions result from Section 533’s conscience protections.

“The Secretary of Defense will ensure that the implementing regulations do not permit or condone discriminatory actions that compromise good order and discipline or otherwise violate military codes of conduct.”

Section 533 of the NDAA provides legal protections for military chaplains, barring the Defense Department from forcing them to perform services which violate their moral or religious beliefs.

“No member of the Armed Forces may -- (1) require a chaplain to perform any rite, ritual, or ceremony that is contrary to the conscience, moral principles, or religious beliefs of the chaplain; or (2) discriminate or take any adverse personnel action against a chaplain, including denial of promotion, schooling, training, or assignment, on the basis of the refusal by the chaplain to comply with a requirement prohibited by paragraph,” the section reads.

Advocates had feared that the military might begin forcing chaplains to perform marriage or civil commitment ceremonies for homosexual service members or civilians in states where such ceremonies are legal – ceremonies which could run afoul of the religious beliefs of those chaplains.

President Obama signed the NDAA into law Wednesday, and while he does not have the power to veto particular sections of a bill – known as a line-item veto – he can issue such signing statements indicating how his administration will interpret its duty to enforce the laws he is signing.

Such statements were used widely by former President George W. Bush, earning scorn from Democrats – including then-Senator Barack Obama (D-Ill.)

“I disagree with that [issuing signing statements],” Obama said in May 2008 while campaigning for president. “I taught the Constitution for 10 years. I believe in the Constitution and I will obey the Constitution of the United States – we’re not going to use signing statements as a way of doing an end-run around Congress.”